Difference between revisions of "Documentation/Nightly/Training"
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− | *The [[Media:3DDataLoadingandVisualization_Slicer4.5_SoniaPujol.pdf | Data loading and 3D visualization]] course guides through the basics of loading and viewing volumes and 3D models in | + | |
− | *Author: Sonia Pujol, Ph.D. | + | * Slicer 4.10 |
− | *Modules: Welcome to Slicer, Sample Data, Models. | + | ** The [http://slicer.kitware.com/midas3/download/item/356408/20180430_DataLoadingAndVisualizationTutorial.pdf Data loading and visualization] ([http://slicer.kitware.com/midas3/download/item/356409/20180430_DataLoadingAndVisualizationTutorial.pptx pptx]) course guides through the basics of loading and viewing volumes and 3D models in Slicer 4.10. |
− | *Audience: End-users | + | ** Author: Csaba Pinter |
− | *Based on: 3D Slicer version 4.5 | + | ** Modules: Welcome to Slicer, Data, Volume Rendering, Models. |
− | *The [http://slicer.kitware.com/midas3/download/?items=330421,1 3DVisualization dataset] contain an MR scan and a series of 3D models of the brain. | + | ** Audience: End-users |
+ | ** Based on: 3D Slicer version 4.10 | ||
+ | ** The [http://slicer.kitware.com/midas3/download/?items=330421,1 3DVisualization dataset] contain an MR scan and a series of 3D models of the brain. | ||
+ | |||
+ | * Slicer 4.5 | ||
+ | ** The [[Media:3DDataLoadingandVisualization_Slicer4.5_SoniaPujol.pdf | Data loading and 3D visualization]] course guides through the basics of loading and viewing volumes and 3D models in Slicer 4.5. | ||
+ | ** Author: Sonia Pujol, Ph.D. | ||
+ | ** Modules: Welcome to Slicer, Sample Data, Models. | ||
+ | ** Audience: End-users | ||
+ | ** Based on: 3D Slicer version 4.5 | ||
+ | ** The [http://slicer.kitware.com/midas3/download/?items=330421,1 3DVisualization dataset] contain an MR scan and a series of 3D models of the brain. | ||
|align="right"| | |align="right"| | ||
+ | [[Image:20180426_DataLoadingAndVisualizationTutorial.png|right|250px|]] | ||
[[Image:Slicer4DataLoading_tutorial.png|right|250px|]] | [[Image:Slicer4DataLoading_tutorial.png|right|250px|]] | ||
|} | |} | ||
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− | == Slicer4 Image | + | == Slicer4 Image Segmentation == |
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* Segmentation for 3D printing: shows how to use the Segment Editor module for combining CAD designed parts with patient-specific models. | * Segmentation for 3D printing: shows how to use the Segment Editor module for combining CAD designed parts with patient-specific models. | ||
** '''[https://discourse.slicer.org/t/new-video-tutorial-for-segment-editor-lumbar-spine-segmentation-for-3d-printing/700 Video tutorial]'''. Author: Hillary Lia. | ** '''[https://discourse.slicer.org/t/new-video-tutorial-for-segment-editor-lumbar-spine-segmentation-for-3d-printing/700 Video tutorial]'''. Author: Hillary Lia. | ||
− | ** '''[ | + | ** '''[[Documentation/{{documentation/version}}/Training#Segmentation_for_3D_printing|Segmentation for 3D printing Step-by-step tutorial]]'''. Author: Csaba Pinter, MSc |
** Audience: Users and developers interested in segmentation and 3D printing | ** Audience: Users and developers interested in segmentation and 3D printing | ||
+ | ** Dataset: [[:File:BasePiece.zip|Phantom base STL model]] Source: [http://perk-software.cs.queensu.ca/plus/doc/nightly/modelcatalog/ PerkLab]. | ||
+ | |align="right"| | ||
+ | [[File:SlicerWinterProjectWeek2017-Segmentation-for-3d-printing.png | 200px]]. | ||
** Based on: 3D Slicer version 4.7 | ** Based on: 3D Slicer version 4.7 | ||
|align="right"|[[Image:20170717_3DPrintingTutorialYoutube.PNG|280px]] | |align="right"|[[Image:20170717_3DPrintingTutorialYoutube.PNG|280px]] | ||
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** Based on: 3D Slicer version 4.8 | ** Based on: 3D Slicer version 4.8 | ||
|align="right"|[[Image:WholeHeartSegYoutube.png|280px]] | |align="right"|[[Image:WholeHeartSegYoutube.png|280px]] | ||
+ | |--- | ||
+ | | | ||
+ | * '''[https://youtu.be/0at15gjk-Ns Video tutorial: Femur and pelvis segmentation from CT]''' shows how to use the Segment Editor module for segmenting pelvis and femur from CT volumes. | ||
+ | ** Author: Andras Lasso, PhD | ||
+ | ** Audience: Users who need to segment bones in CT images for visualization, quantification, or simulation. | ||
+ | ** Sample data set: https://wiki.cancerimagingarchive.net/display/Public/TCGA-PRAD (Subject TCGA-VP-A878) | ||
+ | ** Based on: 3D Slicer version 4.8 | ||
+ | |align="right"|[[Image:FemurSegmentationYoutube.png|280px]] | ||
|} | |} | ||
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− | * The [https:// | + | * The [https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SlicerRT_WorldCongress_TutorialIGRT.pdf SlicerRT tutorial] is an introduction to the Radiation Therapy functionalities of Slicer. |
* Author: Csaba Pinter, Andras Lasso, An Wang, Gregory C. Sharp, David Jaffray, Gabor Fichtinger. | * Author: Csaba Pinter, Andras Lasso, An Wang, Gregory C. Sharp, David Jaffray, Gabor Fichtinger. | ||
* Dataset: [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip download] from MIDAS server | * Dataset: [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip download] from MIDAS server | ||
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− | *The [https:// | + | *The [https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SegmentationFor3DPrinting_TutorialContestWinter2017.pdf Segmentation for 3D printing Tutorial] ([https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SegmentationFor3DPrinting_TutorialContestWinter2017.pptx pptx]) is an introduction to the new [[Documentation/{{documentation/version}}/Modules/SegmentEditor|Segment Editor]] module, demonstrated through the popular topic of 3D printing. |
*Author: Csaba Pinter (Queen's University, Canada) | *Author: Csaba Pinter (Queen's University, Canada) | ||
* [https://www.youtube.com/watch?v=Uht6Fwtr9hE Narrated video version on YouTube]. | * [https://www.youtube.com/watch?v=Uht6Fwtr9hE Narrated video version on YouTube]. | ||
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= External Resources = | = External Resources = | ||
+ | |||
+ | == Resources for Chinese users == | ||
+ | |||
+ | |||
+ | {|width="100%" | ||
+ | | | ||
+ | A 3D Slicer community on WeChat in China offers many tutorials and clinical examples in Chinese. Note that the images are of interest to non-Chinese speakers and Google Translate does a reasonable job of translating some of the text. | ||
+ | |||
+ | * [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486116&idx=1&sn=772e9d431ac32cbb73d08cf0e6bc219a&chksm=eacc0096ddbb89805d93ac4be181d1a35058031bac673d7a91b3b44dccee2bfd1d8461397635#rd Getting started 大脑前动脉远端动脉瘤手术夹闭治疗] | ||
+ | |||
+ | * [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247484787&idx=1&sn=1f6279bdccab168fc79b7275e9fe91ca&chksm=eacc0f41ddbb8657be92f617661133d87bb55a4ecf12f786e97a8b7d5249a05d11e0cd620c3f#rd distal anterior cerebral artery aneurysm 3D Slicer:漂亮得不像实力派] | ||
+ | |||
+ | * [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486360&idx=1&sn=f833b13a26f543aa9175419a03df7f52&chksm=eacc01aaddbb88bcb004773a4db8a9b3c7633d21cda3956f84b96515252eb861c5eb1e75a60b&mpshare=1&scene=24&srcid=0212LIfOkBRm9CvA7ImHCpRt#rd meningioma skull resection 脑膜瘤患者颅骨切除一期修补的3DSlicer方案] | ||
+ | |||
+ | * [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486079&idx=1&sn=9b926dc398a408e3441082b9e0ffde61&chksm=eacc004dddbb895bf9b60f5f1bc443513196e4cb90a6caf6f348a4da7b7fc22eb658661aeb49&mpshare=1&scene=24&srcid=0212AFtT2Wq7K7bvkMGTdyih#rd Cerebral hemorrhage by forehead positioning method 脑出血经额手术定位法(五 ] | ||
+ | |||
+ | * [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247485356&idx=1&sn=044f5899b651b35994db00c32ab688ee&chksm=eacc0d9eddbb8488f16ff82bb1dda8456a4011790fed024781972d578783e67781443cf4a319&mpshare=1&scene=24&srcid=0212G45TadrPnX8tp9eaNXUs#rd Hematoma modeling 血肿建模的第11种方法] | ||
+ | |||
+ | * [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486025&idx=1&sn=b281324893be4ab116d20826f1b426c3&chksm=eacc007bddbb896d9deb096f209278f40c0b52c6410a8a9ff3ce8c3697c99304f18eb678f11e&mpshare=1&scene=24&srcid=02125v1kxvIGmfkxx7mUZcCM#rd Mobile phone positioning and AR application 手机定位及AR应用的初步探索] | ||
+ | |||
+ | |align="right"| | ||
+ | [[image:Wechat-hemorage-2018-02-12.png|250px|Example WeChat tutorial slides]] | ||
+ | |} | ||
+ | |||
+ | == Resources in German == | ||
+ | |||
+ | * [https://www.youtube.com/watch?v=sl-00kGpuPk&list=PLJWCUXz3GeAfmYLiFcKus_c0jcsMnVsgb A series of four YouTube videos on python programming in Slicer] (German narration with English subtitles) | ||
== Murat Maga's blog posts about using 3D Slicer for biology == | == Murat Maga's blog posts about using 3D Slicer for biology == |
Revision as of 14:02, 27 April 2018
Home < Documentation < Nightly < Training
For the latest Slicer documentation, visit the read-the-docs. |
Introduction: Slicer Nightly Tutorials
- This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version Nightly release) to accomplish certain tasks.
- For tutorials for other versions of Slicer, please visit the Slicer training portal.
- For "reference manual" style documentation, please visit the Slicer Nightly documentation page
- For questions related to the Slicer4 Training Compendium, please send an e-mail to Sonia Pujol, Ph.D., Director of Training of 3D Slicer.
- Some of these tutorials are based on older releases of 3D Slicer. The concepts are still useful but bear in mind that some interface elements and features will be different in updated versions.
Contents
- 1 Introduction: Slicer Nightly Tutorials
- 2 General Introduction
- 3 Tutorials for software developers
- 4 Specific functions
- 4.1 Slicer4 Diffusion Tensor Imaging Tutorial
- 4.2 Slicer4 Neurosurgical Planning Tutorial
- 4.3 Slicer4 3D Visualization of DICOM images for Radiology Applications
- 4.4 Slicer4 Quantitative Imaging tutorial
- 4.5 Slicer4 IGT
- 4.6 Slicer4 Image Segmentation
- 4.7 Slicer4 Image Registration
- 4.8 Slicer4 Radiation Therapy Tutorial
- 4.9 Other
- 5 3D Slicer Tutorial contests
- 6 Additional resources
- 7 External Resources
General Introduction
Slicer Welcome Tutorial
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Slicer4Minute Tutorial
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Slicer4 Data Loading and 3D Visualization
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Tutorials for software developers
Slicer4 Programming Tutorial
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For additional Python scripts examples, please visit the Script Repository page
Developing and contributing extensions for 3D Slicer
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Specific functions
Slicer4 Diffusion Tensor Imaging Tutorial
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Slicer4 Neurosurgical Planning Tutorial
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Slicer4 3D Visualization of DICOM images for Radiology Applications
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Slicer4 Quantitative Imaging tutorial
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Slicer4 IGT
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Slicer4 Image Segmentation
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Slicer4 Image Registration
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- Based on: 3D Slicer version 4.5
See the Registration Library for worked out registration examples with data.
Slicer4 Radiation Therapy Tutorial
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Other
Additional (non-curated) videos-based demonstrations using 3D Slicer are accessible on You Tube.
3D Slicer Tutorial contests
Winter 2017 Tutorial contest
Segmentation for 3D printing
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Slicer Pathology
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Simple Python Tool for Quality Control of DWI data
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SPHARM-PDM
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Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink
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Fiber Bundle Volume Measurement
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Winter 2016 Tutorial contest
Subject Hierarchy
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Fiber Bundle Selection and Scalar Measurements
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Plastimatch
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UKF
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Summer 2014 Tutorial contest
Cardiac Agatston Tutorial
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CMR Toolkit LA workflow
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Summer 2013 Tutorial contest
Cardiac MRI Toolkit
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HelloCLI
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SlicerRT
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DTIPrep
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Summer 2012 Tutorial contest
Automatic Left Atrial Scar Segmenter
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Qualitative and quantitative comparison of two RT dose distributions
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Dose accumulation for adaptive radiation therapy
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WebGL Export
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OpenIGTLink
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Additional resources
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External Resources
Resources for Chinese users
A 3D Slicer community on WeChat in China offers many tutorials and clinical examples in Chinese. Note that the images are of interest to non-Chinese speakers and Google Translate does a reasonable job of translating some of the text. |
Resources in German
- A series of four YouTube videos on python programming in Slicer (German narration with English subtitles)
Murat Maga's blog posts about using 3D Slicer for biology
Using the (legacy) Editor
Fast GrowCut
|
Use case: Slicer in paleontology
This set of tutorials about the use of slicer in paleontology is very well written and provides step-by-step instructions. Even though it covers slicer version 3.4, many of the concepts and techniques have applicability to the new version and to any 3D imaging field:
- Open Source Paleontologist: 3D Slicer: The Tutorial
- Open Source Paleontologist: 3D Slicer: The Tutorial Part II
- Open Source Paleontologist: 3D Slicer: The Tutorial Part III
- Open Source Paleontologist: 3D Slicer: The Tutorial Part IV
- Open Source Paleontologist: 3D Slicer: The Tutorial Part V
- Open Source Paleontologist: 3D Slicer: The Tutorial Part VI
Team Contributions
See the collection of videos on the Kitware vimeo album.
User Contributions
See the User Contributions Page for more content.